Logo-Sequence Generator for RNA-Immunoprecipitation followed by sequencing

Interdisciplinary Center for Clinical Research - RWTH-Aachen

Table of Contents

1. 1. Table of top abundant transcripts (FPKM > 1)
2. 2. Sequences and annotation
3. 3. Generation of motif instances
4. 4. Generation of match data
5. 5. Generation of sequence Logos

1. Table of top abundant transcripts (FPKM >= 1)

Keep transcripts with predicted FPKM greater or equal to 1 in either of both conditions (hnRNPL vs. InputKG1a)—furthermore, remove transcripts with a non-positive log of FPKM ratio. Here called L2FC. This is possible are not all transcripts in the list of top genes must be upregulated (L2FC >= 1).

2. Sequences and Annotation

Metadata based on gene id

Metadata based on available mRNA sequences

Metadata based on available lncRNA sequences

Summary on available regions in top transcripts

3. Generation of Motif Instances

Interaction Motifs

Interaction Motifs (no critical Gs)

Regulatory Motifs

4. Generation of Match Data

3-UTR

3-UTR (no critical Gs)

5-UTR

5-UTR (no critical Gs)

CDS

CDS (no critical Gs)

lncRNA

lncRNA (no critical Gs)

5. Generation of Sequence Logos

5.1 Interaction

All (Summary)

All (Detailed)

3-UTR (Summary)

3-UTR (Detailed)

5-UTR (Summary)

5-UTR (Detailed)

CDS (Summary)

CDS (Detailed)

Non Coding RNA

Session Info

R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.7.1
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.7.1

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=de_DE.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=de_DE.UTF-8    LC_MESSAGES=en_US.UTF-8    LC_PAPER=de_DE.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=de_DE.UTF-8
[12] LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] forcats_0.5.0     stringr_1.4.0     dplyr_1.0.2       purrr_0.3.4       readr_1.4.0       tidyr_1.1.2       tibble_3.0.4      tidyverse_1.3.0   genefilter_1.72.0 cowplot_1.1.0     ggseqlogo_0.1     ggplot2_3.3.3     DT_0.16           biomaRt_2.46.0   

loaded via a namespace (and not attached):
  [1] colorspace_2.0-0            ggsignif_0.6.1              ellipsis_0.3.1              rio_0.5.16                  XVector_0.30.0              fs_1.5.0                    GenomicRanges_1.42.0        rstudioapi_0.13             ggpubr_0.4.0                farver_2.0.3               
 [11] ggrepel_0.9.0               bit64_4.0.5                 fansi_0.4.1                 AnnotationDbi_1.52.0        lubridate_1.7.9.2           xml2_1.3.2                  splines_4.0.3               geneplotter_1.68.0          knitr_1.30                  jsonlite_1.7.2             
 [21] broom_0.7.3                 annotate_1.68.0             dbplyr_2.0.0                pheatmap_1.0.12             BiocManager_1.30.10         compiler_4.0.3              httr_1.4.2                  rvcheck_0.1.8               backports_1.2.1             assertthat_0.2.1           
 [31] Matrix_1.3-0                cli_2.2.0                   htmltools_0.5.0             prettyunits_1.1.1           tools_4.0.3                 gtable_0.3.0                glue_1.4.2                  GenomeInfoDbData_1.2.4      rappdirs_0.3.1              tinytex_0.28               
 [41] Rcpp_1.0.5                  carData_3.0-4               Biobase_2.50.0              cellranger_1.1.0            vctrs_0.3.6                 crosstalk_1.1.0.1           xfun_0.19                   rvest_0.3.6                 openxlsx_4.2.3              lifecycle_0.2.0            
 [51] rstatix_0.6.0               XML_3.99-0.5                zlibbioc_1.36.0             scales_1.1.1                hms_0.5.3                   MatrixGenerics_1.2.0        parallel_4.0.3              SummarizedExperiment_1.20.0 RColorBrewer_1.1-2          yaml_2.2.1                 
 [61] curl_4.3                    memoise_1.1.0               stringi_1.5.3               RSQLite_2.2.1               S4Vectors_0.28.1            BiocGenerics_0.36.0         zip_2.1.1                   BiocParallel_1.24.1         GenomeInfoDb_1.26.2         rlang_0.4.9                
 [71] pkgconfig_2.0.3             matrixStats_0.58.0          bitops_1.0-6                lattice_0.20-41             htmlwidgets_1.5.3           labeling_0.4.2              bit_4.0.4                   tidyselect_1.1.0            magrittr_2.0.1              DESeq2_1.30.0              
 [81] R6_2.5.0                    IRanges_2.24.1              generics_0.1.0              DelayedArray_0.16.0         DBI_1.1.0                   pillar_1.4.7                haven_2.3.1                 foreign_0.8-81              withr_2.3.0                 survival_3.2-7             
 [91] abind_1.4-5                 RCurl_1.98-1.2              modelr_0.1.8                crayon_1.3.4                car_3.0-10                  BiocFileCache_1.14.0        progress_1.2.2              locfit_1.5-9.4              grid_4.0.3                  readxl_1.3.1               
[101] data.table_1.13.4           blob_1.2.1                  reprex_0.3.0                digest_0.6.27               xtable_1.8-4                gridGraphics_0.5-1          openssl_1.4.3               stats4_4.0.3                munsell_0.5.0               ggplotify_0.0.5            
[111] askpass_1.1